Disease classification

Number

Percent

control

77

41.0

RA

55

29.3

SLE

56

29.8

Differential Gene Expression

Comparison

# Up
regulated

% Up
regulated

# Down
regulated

% Down
regulated

Mean count
cutoff

# Low
counts

% Low
counts

RA vs control

1690

4.35

1886

4.85

2

18285

47.01

SLE vs control

2248

5.78

2377

6.11

2

17538

45.09

25 genes with largest negative log-fold change in experimental group

## 

RA_vs_control

Gene

Log2-fold change

Log-fold change
standard error

P-value*

Adjusted
P-value

HSPA1B

7.5

0.42

6.3e-75

6.5e-71

HSPA6

7

0.50

1.0e-55

5.2e-52

HSPA1A

6.8

0.39

1.8e-79

3.6e-75

AL671762.1

6.2

0.39

4.1e-61

2.8e-57

GJB2

5.2

1.20

6.5e-06

1.8e-04

CCL22

5

0.77

6.8e-13

1.3e-10

MIR210HG

4.5

0.88

6.1e-15

2.0e-12

HSPB1

3.6

0.29

3.5e-40

1.2e-36

LINC00656

3.4

1.00

7.5e-04

8.2e-03

SNORD14E

3.1

0.51

3.0e-11

4.2e-09

THBS1

3.1

0.38

5.6e-19

3.4e-16

AC016168.2

3

0.95

1.8e-04

2.7e-03

CREM

3

0.25

1.5e-32

3.9e-29

ERRFI1

3

0.46

9.6e-14

2.3e-11

HSPH1

2.9

0.27

1.1e-30

2.3e-27

AC105105.1

2.8

0.72

1.7e-06

5.6e-05

DNAJB1

2.8

0.20

2.6e-46

1.1e-42

LIF

2.8

0.57

3.0e-09

2.3e-07

SLC6A8

2.7

0.44

2.7e-12

4.8e-10

PHLDB1

2.5

0.55

5.2e-08

2.8e-06

ADM

2.4

0.38

3.1e-12

5.2e-10

DNAH17

2.4

0.60

1.3e-07

6.1e-06

YPEL4

2.4

0.43

7.1e-11

8.6e-09

ATF3

2.3

0.24

2.4e-23

2.5e-20

NGFR

2.3

0.69

8.0e-06

2.1e-04

*Wald test p-values

Benjamini–Hochberg adjusted value

SLE_vs_control

Gene

Log2-fold change

Log-fold change
standard error

P-value*

Adjusted
P-value

HSPA1B

7.1

0.41

7.1e-67

7.6e-63

HSPA1A

6.6

0.39

9.7e-76

2.1e-71

TFPI2

6.1

3.00

4.9e-08

2.4e-06

CCL22

4.8

0.78

2.0e-12

3.5e-10

MIR210HG

4.7

0.80

4.7e-16

1.7e-13

AC011498.4

4.6

0.94

5.0e-11

6.3e-09

AP000941.1

4.5

1.40

1.5e-04

1.8e-03

SEMA6B

4.3

0.55

3.7e-17

1.7e-14

CBARP

4.2

1.00

5.9e-06

1.3e-04

LINC02029

4

1.20

2.1e-04

2.3e-03

HCG20

3.6

0.96

1.0e-04

1.3e-03

AC112496.1

3.5

0.85

1.3e-04

1.5e-03

HILPDA

3.5

0.75

1.9e-13

4.2e-11

SERPINB2

3.3

0.65

2.0e-09

1.6e-07

THBS1

3.3

0.41

9.1e-21

6.5e-18

OLR1

3.2

0.62

6.1e-10

5.7e-08

ABHD17AP6

3.1

1.10

2.4e-03

1.6e-02

CXCL5

3.1

1.20

3.1e-07

1.1e-05

HSPH1

3.1

0.26

7.1e-35

2.2e-31

NRG1

3

0.63

5.9e-10

5.5e-08

SNORD14E

3

0.51

7.9e-11

9.3e-09

HSPB1

2.9

0.29

4.6e-26

7.6e-23

TRPV3

2.9

0.66

2.3e-08

1.3e-06

DNAJB1

2.8

0.20

9.4e-46

4.0e-42

GRIN3B

2.8

0.73

7.2e-07

2.3e-05

*Wald test p-values

Benjamini–Hochberg adjusted value

25 genes with largest positive log-fold change in experimental group

## 

RA_vs_control

Gene

Log2-fold change

Log-fold change
standard error

P-value*

Adjusted
P-value

ACVRL1

4.9

0.86

5.2e-12

8.2e-10

TRBV12-4

4.3

0.91

6.8e-06

1.8e-04

IGLV9-49

4.1

0.79

8.7e-10

7.8e-08

HBB

3.7

0.88

7.0e-07

2.7e-05

ARLNC1

3.5

1.30

2.2e-03

1.8e-02

IGKV1-17

3.5

0.51

3.0e-14

8.3e-12

IGKV2D-28

3.5

0.49

3.9e-16

1.5e-13

IGLV2-5

3.5

0.83

3.6e-04

4.6e-03

TMEM198

3.5

0.91

2.5e-07

1.1e-05

TNFRSF17

3.5

0.52

3.3e-13

7.3e-11

IGLV3-19

3.4

0.50

9.0e-14

2.2e-11

AL162724.1

3.3

0.82

5.7e-06

1.6e-04

IGHV2-70D

3.3

0.80

7.9e-06

2.1e-04

TRBV5-1

3.2

0.57

5.6e-11

7.0e-09

TRBV7-6

3.2

0.83

6.3e-04

7.1e-03

FAM171A1

3.1

0.64

1.3e-07

6.1e-06

FAM218A

3.1

0.93

5.0e-04

6.0e-03

LINC00402

3.1

0.67

3.4e-07

1.4e-05

LINC02033

3

0.64

4.7e-07

1.9e-05

AL392172.2

2.9

1.30

3.0e-03

2.3e-02

AP001107.9

2.9

0.60

3.5e-08

2.0e-06

IGHV1-69D

2.9

0.53

1.2e-10

1.4e-08

IGLC6

2.9

0.99

1.6e-03

1.5e-02

RPL23AP81

2.9

0.73

3.1e-05

6.5e-04

FAM238B

2.8

0.94

2.4e-04

3.3e-03

HBA1

2.8

0.82

2.5e-05

5.4e-04

IGHV4-55

2.8

0.78

1.2e-05

3.0e-04

*Wald test p-values

Benjamini–Hochberg adjusted value

SLE_vs_control

Gene

Log2-fold change

Log-fold change
standard error

P-value*

Adjusted
P-value

IFI27

6.1

0.69

2.3e-21

1.8e-18

ELOVL6

5

0.93

3.9e-13

8.0e-11

IGLVI-70

4.7

1.00

2.9e-06

7.3e-05

CERS3

3.6

0.84

4.6e-06

1.1e-04

IGHGP

3.6

0.61

1.0e-10

1.2e-08

OTOF

3.3

0.59

6.3e-11

7.6e-09

Z99756.1

3.2

0.91

2.7e-06

6.8e-05

LINC00487

3.1

0.76

6.8e-08

3.2e-06

RTEL1P1

3.1

0.80

1.8e-06

4.8e-05

STOX1

3

0.85

4.0e-05

6.1e-04

IFI44L

2.9

0.30

1.3e-23

1.6e-20

IGLV7-46

2.8

0.56

3.2e-09

2.3e-07

AL512353.1

2.7

0.91

1.9e-05

3.4e-04

CYP2J2

2.7

0.94

3.0e-03

1.9e-02

IGHG1

2.6

0.31

1.1e-19

7.4e-17

LY6E-DT

2.6

0.72

4.5e-06

1.0e-04

USP18

2.6

0.41

8.0e-12

1.2e-09

C11orf45

2.5

0.88

4.7e-04

4.5e-03

IGHV1-69

2.5

0.57

9.2e-08

4.1e-06

KCNG1

2.5

0.81

4.7e-05

7.1e-04

LINC02033

2.5

0.65

1.2e-05

2.3e-04

NRIR

2.5

0.51

1.4e-08

8.4e-07

RUFY4

2.5

0.49

1.9e-10

2.0e-08

SIGLEC1

2.5

0.48

6.0e-09

4.0e-07

AC009686.2

2.4

0.74

5.2e-04

4.8e-03

ACTA2-AS1

2.4

0.64

2.6e-05

4.4e-04

TLDC2

2.4

0.77

2.0e-06

5.4e-05

*Wald test p-values

Benjamini–Hochberg adjusted value

Expression of top class DE genes by class

Sorted by disease classification

Sorted by cluster

Sorted by hierarchical clustering

Expression of all top DE genes

Sorted by disease classification

Sorted by cell type

Sorted by cluster

Sorted by hierarchical clustering

Volcano plot of gene expression

## Warning: Removed 18286 rows containing missing values (geom_point).

## Warning: Removed 17539 rows containing missing values (geom_point).

Expression of selected interferon-stimulated genes

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

Expression of individual genes in the M1.2, M3.4, and M5.12 gene modules

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

Sample Clustering

The eigenvales for the annotated Banchereau modules were used to calculate an adjacentcy matrix, which was in turn used to calculate the gap statistic to determine the optimal k-clusters.

## `summarise()` regrouping output by 'disease_class' (override with `.groups` argument)

Clustering and variation of samples in reduced dimensional space

PCA

PCA by disease classification

PCA by cell type

PCA by ethnicity

PCA by K-means cluster

UMAP

UMAP by disease classification

UMAP by cell type

UMAP by ethnicity

UMAP by K-means cluster

Module scores

SLE Interferon module scores

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

SLE Inflammatory module scores

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

Low-density granulocyte module scores

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

SLE Modules with an annotated associated pathway

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

All SLE modules

## ℹ No targets to load in loadd().

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

Expression of the annotated Banchereau modules

By disease classification

By cell_type

By cluster

WGCNA

Expression similarity dendrogram

Expression of identified modules

By disease classification

## Warning: Removed 1 rows containing non-finite values (stat_bracket).

## Warning: Removed 1 rows containing non-finite values (stat_bracket).

## Warning: Removed 1 rows containing non-finite values (stat_bracket).

By cell_type

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

By cluster

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

## Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique 'x' values

WGCNA eigenvalues

Sorted by disease classification

Sorted by cell_type

Sorted by cluster

Sorted by hierarchical clustering

Gene ontology GSEA of WGCNA modules

Use of WGCNA modules in classifying clusters.

The module eigengene scores were used to train a random forest model with repeated cross validation to predict cluster identity.

The model was trained with 75% of the dataset and tested on 25%.

Note: Subjects with LP were excluded due to the small population size.

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction 1 2 3 4 5 6 7 8
##          1 5 0 0 0 0 5 0 0
##          2 0 4 0 1 0 0 0 0
##          3 0 0 0 0 0 0 0 0
##          4 0 6 1 9 0 0 0 0
##          5 0 0 0 0 0 0 2 1
##          6 1 0 0 0 0 3 1 0
##          7 0 0 0 0 0 0 1 1
##          8 0 0 0 0 0 0 4 1
## 
## Overall Statistics
##                                         
##                Accuracy : 0.5           
##                  95% CI : (0.349, 0.651)
##     No Information Rate : 0.2174        
##     P-Value [Acc > NIR] : 2.259e-05     
##                                         
##                   Kappa : 0.4039        
##                                         
##  Mcnemar's Test P-Value : NA            
## 
## Statistics by Class:
## 
##                      Class: 1 Class: 2 Class: 3 Class: 4 Class: 5 Class: 6 Class: 7 Class: 8
## Sensitivity            0.8333  0.40000  0.00000   0.9000       NA  0.37500  0.12500  0.33333
## Specificity            0.8750  0.97222  1.00000   0.8056  0.93478  0.94737  0.97368  0.90698
## Pos Pred Value         0.5000  0.80000      NaN   0.5625       NA  0.60000  0.50000  0.20000
## Neg Pred Value         0.9722  0.85366  0.97826   0.9667       NA  0.87805  0.84091  0.95122
## Prevalence             0.1304  0.21739  0.02174   0.2174  0.00000  0.17391  0.17391  0.06522
## Detection Rate         0.1087  0.08696  0.00000   0.1957  0.00000  0.06522  0.02174  0.02174
## Detection Prevalence   0.2174  0.10870  0.00000   0.3478  0.06522  0.10870  0.04348  0.10870
## Balanced Accuracy      0.8542  0.68611  0.50000   0.8528       NA  0.66118  0.54934  0.62016

The relative importance of each eigengene in classification:

## parRF variable importance
## 
##   variables are sorted by maximum importance across the classes
##   only 20 most important variables shown (out of 22)
## 
##                      1        2        3      4        5        6     7       8
## MEblue         14.3693  7.82545 -0.97829  8.095  0.88383  6.71602 6.422  4.4448
## MEturquoise     8.5627  5.71845 -1.88396 14.235  0.06745  1.63373 1.897  7.3597
## MEpink         11.5824  3.81770 -0.26493  6.681 -0.07100  3.47044 2.054  0.8572
## MEgrey60       11.5603  6.03835 -0.62524  6.218  1.83138  5.78396 5.676  1.3140
## MEmidnightblue 11.2442  5.38447  0.11599  7.883 -1.72204  0.90253 8.619  6.1353
## MEbrown         9.9589  6.41273 -3.25380 10.646  0.22458  4.94336 6.648  4.9923
## MEpurple        6.7482 -2.21446 -2.26207 10.334  1.53567  1.47778 5.543  1.2884
## MEcyan          5.9730  1.99198 -2.14758 10.267  0.22573  0.08171 7.071  4.2144
## MEblack         6.5315  4.94709 -2.44302 10.115  3.34137  0.32909 1.586 -1.8805
## MEyellow        7.5887  5.58255  1.05781  9.419  0.59289  1.83879 2.558  5.0972
## MEtan           7.1845  4.15669  0.03735  7.270  0.01082  0.50122 4.931  8.3790
## MElightyellow   8.1430  2.42064  1.70996  5.354  1.69733  2.54109 6.027  3.5652
## MEred           7.7584  3.77223 -1.78087  6.651  1.01509  0.54880 6.746  5.6750
## MEdarkred       7.4979  1.85037 -2.61042  6.125  0.31279  1.61495 5.423  1.1253
## MEgreenyellow   4.1659 -0.03084 -2.64787  6.788 -0.74295  2.01727 2.987  2.8514
## MEgreen         6.1628  5.94511 -2.27799  4.344 -0.14282 -1.52697 1.140  1.0719
## MElightgreen    6.0871 -3.06843 -0.28870  2.069 -0.77411 -2.03344 2.961  1.3398
## MEdarkgreen    -0.2039  1.89077 -2.10168  2.749 -0.32412  0.55297 5.400 -3.7847
## MEsalmon        5.3525  3.63849  1.01297  3.311  0.08243 -1.30895 1.571  0.4298
## MElightcyan     2.5020  2.61766  0.16440  5.170  1.37282 -0.82609 2.747 -0.2886

Use of WGCNA modules in labeling disease class.

The module eigengene scores were used to train a random forest model with repeated cross validation to predict cluster identity.

The model was trained with 75% of the dataset and tested on 25%.

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction control RA SLE
##    control      16  2   1
##    RA            2  5   8
##    SLE           1  6   5
## 
## Overall Statistics
##                                           
##                Accuracy : 0.5652          
##                  95% CI : (0.4111, 0.7107)
##     No Information Rate : 0.413           
##     P-Value [Acc > NIR] : 0.02666         
##                                           
##                   Kappa : 0.3391          
##                                           
##  Mcnemar's Test P-Value : 0.96269         
## 
## Statistics by Class:
## 
##                      Class: control Class: RA Class: SLE
## Sensitivity                  0.8421    0.3846     0.3571
## Specificity                  0.8889    0.6970     0.7812
## Pos Pred Value               0.8421    0.3333     0.4167
## Neg Pred Value               0.8889    0.7419     0.7353
## Prevalence                   0.4130    0.2826     0.3043
## Detection Rate               0.3478    0.1087     0.1087
## Detection Prevalence         0.4130    0.3261     0.2609
## Balanced Accuracy            0.8655    0.5408     0.5692

The relative importance of each eigengene in classification:

## parRF variable importance
## 
##   only 20 most important variables shown (out of 22)
## 
##                Overall
## MElightgreen    25.735
## MEroyalblue      5.533
## MElightcyan      5.029
## MEred            4.408
## MEdarkgreen      3.831
## MElightyellow    3.762
## MEcyan           3.433
## MEgrey60         3.403
## MEblack          3.382
## MEtan            3.289
## MEsalmon         3.213
## MEgreenyellow    3.166
## MEblue           2.976
## MEgreen          2.948
## MEdarkred        2.877
## MEmidnightblue   2.718
## MEmagenta        2.417
## MEpurple         2.357
## MEyellow         2.271
## MEbrown          2.206

Use of module modules in classifying clusters.

The module eigengene scores were used to train a random forest model with repeated cross validation to predict cluster identity.

The model was trained with 75% of the dataset and tested on 25%.

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction 1 2 3 4 5 6 7 8
##          1 6 0 0 0 0 3 0 0
##          2 0 5 0 4 0 0 0 0
##          3 0 0 0 0 0 0 0 0
##          4 0 3 0 7 0 0 0 0
##          5 0 0 0 0 0 0 0 0
##          6 1 0 0 0 0 4 0 0
##          7 0 0 0 0 1 0 4 2
##          8 0 0 0 0 0 0 3 2
## 
## Overall Statistics
##                                           
##                Accuracy : 0.6222          
##                  95% CI : (0.4654, 0.7623)
##     No Information Rate : 0.2444          
##     P-Value [Acc > NIR] : 8.541e-08       
##                                           
##                   Kappa : 0.5436          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: 1 Class: 2 Class: 3 Class: 4 Class: 5 Class: 6 Class: 7 Class: 8
## Sensitivity            0.8571   0.6250       NA   0.6364  0.00000  0.57143  0.57143  0.50000
## Specificity            0.9211   0.8919        1   0.9118  1.00000  0.97368  0.92105  0.92683
## Pos Pred Value         0.6667   0.5556       NA   0.7000      NaN  0.80000  0.57143  0.40000
## Neg Pred Value         0.9722   0.9167       NA   0.8857  0.97778  0.92500  0.92105  0.95000
## Prevalence             0.1556   0.1778        0   0.2444  0.02222  0.15556  0.15556  0.08889
## Detection Rate         0.1333   0.1111        0   0.1556  0.00000  0.08889  0.08889  0.04444
## Detection Prevalence   0.2000   0.2000        0   0.2222  0.00000  0.11111  0.15556  0.11111
## Balanced Accuracy      0.8891   0.7584       NA   0.7741  0.50000  0.77256  0.74624  0.71341

The relative importance of each eigengene in classification:

## parRF variable importance
## 
##   variables are sorted by maximum importance across the classes
##   only 20 most important variables shown (out of 260)
## 
##             1       2          3       4       5       6       7       8
## M9.50  1.3644  1.3989  2.309e-01  0.0000  7.9646 -1.4095 -2.2869 16.6677
## M5.15 14.9597  2.6251  3.377e+00  8.3911  6.1483  3.4568  9.8552  8.5809
## M8.22  1.3281 12.3497 -2.536e+00  1.2379 -1.7922  1.0010  2.2928  1.7264
## M8.54 11.0772  0.1854  6.404e-01  1.0010  0.0000 -4.1093  0.1562  0.0000
## M4.1   9.4637  9.7319 -3.584e+00 10.9203  5.1621  7.1675  7.4282  8.2874
## M8.41  8.2247 10.2774 -5.887e+00 10.3112  3.7191  6.8320  9.5280  8.4319
## M4.15  9.0549  8.7563 -1.581e+00  9.8181  4.5581  4.7102  7.7209  7.9695
## M6.13  2.5102  1.1739  2.577e+00  2.7801  1.0910 -1.9585 -1.0567  8.4132
## M8.58  8.0103  4.3608  2.869e+00  4.8290  4.0826  8.2278  3.0940  5.4960
## M5.14  3.5232 -2.8498 -1.143e+00  7.8671  1.9599  2.2626  2.2390  3.6788
## M7.17  2.7396 -4.3366  4.230e-17  7.2724  1.6691  3.2706  2.7833  2.9750
## M9.30  7.1216 -0.2774  2.898e+00  1.0010  4.0843  3.9310  5.5550  5.9115
## M6.16  0.8473 -3.9059 -1.344e+00  7.0236  0.3180  0.5205  1.3714  1.7241
## M8.71  6.9733  1.6374  1.327e+00  1.3910  4.6504  4.5508  6.8717  6.2373
## M9.24  6.2781 -3.8498  1.214e+00  5.8269  0.1690 -0.8202  1.0694  5.3447
## M9.15  1.6271 -1.9084 -1.001e+00  5.9538  1.4171  1.1688  1.7262  1.5498
## M8.56  5.6236  0.4820 -8.464e-01  1.3773  3.3963  4.7765  3.0064  4.6920
## M7.29  1.0010  0.8445  3.848e+00  2.3988  1.9396  0.9768  5.3479  4.3251
## M4.3   1.0010  5.2245  1.178e+00  0.1366  0.0000  1.0010 -0.7752  0.4845
## M6.6   3.5675  3.4052 -9.351e-01  4.8004  0.4658  3.4305  5.1912  4.1304

Use of module modules in labeling disease class.

The module eigengene scores were used to train a random forest model with repeated cross validation to predict cluster identity.

The model was trained with 75% of the dataset and tested on 25%.

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction control RA SLE
##    control      16  3   1
##    RA            2  6   7
##    SLE           1  4   6
## 
## Overall Statistics
##                                           
##                Accuracy : 0.6087          
##                  95% CI : (0.4537, 0.7491)
##     No Information Rate : 0.413           
##     P-Value [Acc > NIR] : 0.005811        
##                                           
##                   Kappa : 0.403           
##                                           
##  Mcnemar's Test P-Value : 0.796853        
## 
## Statistics by Class:
## 
##                      Class: control Class: RA Class: SLE
## Sensitivity                  0.8421    0.4615     0.4286
## Specificity                  0.8519    0.7273     0.8438
## Pos Pred Value               0.8000    0.4000     0.5455
## Neg Pred Value               0.8846    0.7742     0.7714
## Prevalence                   0.4130    0.2826     0.3043
## Detection Rate               0.3478    0.1304     0.1304
## Detection Prevalence         0.4348    0.3261     0.2391
## Balanced Accuracy            0.8470    0.5944     0.6362

The relative importance of each eigengene in classification:

## parRF variable importance
## 
##   variables are sorted by maximum importance across the classes
##   only 20 most important variables shown (out of 260)
## 
##         control       RA     SLE
## M2.3   13.93671  7.46191  5.7414
## M3.4    5.22186 -2.15418  8.1796
## M8.77   3.56442  7.05577  0.1395
## M8.98   6.93188  4.85291  0.9418
## M8.10   5.70636  3.49268  1.3072
## M8.93   4.75082  0.10196  3.7531
## M5.12   3.20252  1.13290  4.7210
## M1.2    4.32166  0.27341  4.3726
## M7.1    0.13589  4.31162 -0.8437
## M8.87   0.88386  4.10724  0.7403
## M4.8    3.80243  0.12635  2.0789
## M4.11   3.75735  0.02174  1.9477
## M9.23   0.93460 -1.00056  3.7241
## M8.86   0.06736  3.57070 -1.2428
## M8.6    1.82644 -1.85412  3.4964
## M7.16   1.85245  3.34325  0.6618
## M8.110  3.30882  0.80783 -0.8009
## M6.3    3.28167  0.56511  2.3193
## M9.10   1.37740  3.23515 -1.4084
## M8.44   3.22465 -0.82291  1.4468
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 4.0.0 (2020-04-24)
##  os       Ubuntu 18.04.4 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Etc/UTC                     
##  date     2020-10-08                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package              * version    date       lib source                                   
##  abind                  1.4-5      2016-07-21 [1] RSPM (R 4.0.0)                           
##  acepack                1.4.1      2016-10-29 [1] RSPM (R 4.0.0)                           
##  annotate               1.66.0     2020-04-27 [1] Bioconductor                             
##  AnnotationDbi          1.50.3     2020-07-25 [1] Bioconductor                             
##  assertthat             0.2.1      2019-03-21 [1] RSPM (R 4.0.0)                           
##  backports              1.1.7      2020-05-13 [1] RSPM (R 4.0.0)                           
##  base64enc              0.1-3      2015-07-28 [1] RSPM (R 4.0.0)                           
##  base64url              1.4        2018-05-14 [1] RSPM (R 4.0.0)                           
##  bayesplot              1.7.2      2020-05-28 [1] RSPM (R 4.0.0)                           
##  bibtex                 0.4.2.2    2020-01-02 [1] RSPM (R 4.0.0)                           
##  Biobase              * 2.48.0     2020-04-27 [1] Bioconductor                             
##  BiocGenerics         * 0.34.0     2020-04-27 [1] Bioconductor                             
##  BiocManager          * 1.30.10    2019-11-16 [1] CRAN (R 4.0.0)                           
##  BiocParallel         * 1.22.0     2020-04-27 [1] Bioconductor                             
##  bit                    1.1-15.2   2020-02-10 [1] RSPM (R 4.0.0)                           
##  bit64                  0.9-7      2017-05-08 [1] RSPM (R 4.0.0)                           
##  bitops                 1.0-6      2013-08-17 [1] RSPM (R 4.0.0)                           
##  blob                   1.2.1      2020-01-20 [1] RSPM (R 4.0.0)                           
##  boot                   1.3-25     2020-04-26 [2] RSPM (R 4.0.0)                           
##  broom                * 0.5.6      2020-04-20 [1] RSPM (R 4.0.0)                           
##  callr                  3.4.3      2020-03-28 [1] RSPM (R 4.0.0)                           
##  car                    3.0-8      2020-05-21 [1] RSPM (R 4.0.0)                           
##  carData                3.0-4      2020-05-22 [1] RSPM (R 4.0.0)                           
##  caret                * 6.0-86     2020-03-20 [1] RSPM (R 4.0.0)                           
##  cellranger             1.1.0      2016-07-27 [1] RSPM (R 4.0.0)                           
##  checkmate              2.0.0      2020-02-06 [1] RSPM (R 4.0.0)                           
##  class                  7.3-17     2020-04-26 [2] RSPM (R 4.0.0)                           
##  cli                    2.0.2      2020-02-28 [1] RSPM (R 4.0.0)                           
##  cluster              * 2.1.0      2019-06-19 [1] RSPM (R 4.0.0)                           
##  clusterProfiler      * 3.16.1     2020-08-18 [1] Bioconductor                             
##  codetools              0.2-16     2018-12-24 [2] CRAN (R 4.0.0)                           
##  colorspace             1.4-1      2019-03-18 [1] RSPM (R 4.0.0)                           
##  colourpicker           1.0        2017-09-27 [1] RSPM (R 4.0.0)                           
##  corrplot             * 0.84       2017-10-16 [1] RSPM (R 4.0.0)                           
##  cowplot              * 1.0.0      2019-07-11 [1] RSPM (R 4.0.0)                           
##  crayon                 1.3.4      2017-09-16 [1] RSPM (R 4.0.0)                           
##  crosstalk              1.1.0.1    2020-03-13 [1] RSPM (R 4.0.0)                           
##  curl                   4.3        2019-12-02 [1] RSPM (R 4.0.0)                           
##  data.table             1.12.8     2019-12-09 [1] RSPM (R 4.0.0)                           
##  DBI                    1.1.0      2019-12-15 [1] RSPM (R 4.0.0)                           
##  dbplyr                 1.4.4      2020-05-27 [1] RSPM (R 4.0.0)                           
##  DelayedArray         * 0.14.1     2020-07-14 [1] Bioconductor                             
##  DESeq2               * 1.28.1     2020-05-12 [1] Bioconductor                             
##  dials                * 0.0.6      2020-04-03 [1] RSPM (R 4.0.0)                           
##  DiceDesign             1.8-1      2019-07-31 [1] RSPM (R 4.0.0)                           
##  digest                 0.6.25     2020-02-23 [1] RSPM (R 4.0.0)                           
##  DO.db                  2.9        2020-09-18 [1] Bioconductor                             
##  doParallel             1.0.15     2019-08-02 [1] RSPM (R 4.0.0)                           
##  DOSE                   3.14.0     2020-04-27 [1] Bioconductor                             
##  downloader             0.4        2015-07-09 [1] RSPM (R 4.0.0)                           
##  dplyr                * 1.0.0      2020-05-29 [1] RSPM (R 4.0.0)                           
##  drake                * 7.12.2     2020-06-02 [1] RSPM (R 4.0.0)                           
##  DT                     0.13       2020-03-23 [1] RSPM (R 4.0.0)                           
##  dygraphs               1.1.1.6    2018-07-11 [1] RSPM (R 4.0.0)                           
##  dynamicTreeCut       * 1.63-1     2016-03-11 [1] RSPM (R 4.0.0)                           
##  e1071                  1.7-3      2019-11-26 [1] RSPM (R 4.0.0)                           
##  edgeR                  3.30.3     2020-06-02 [1] Bioconductor                             
##  ellipsis               0.3.1      2020-05-15 [1] RSPM (R 4.0.0)                           
##  enrichplot             1.8.1      2020-04-29 [1] Bioconductor                             
##  europepmc              0.4        2020-05-31 [1] RSPM (R 4.0.0)                           
##  evaluate               0.14       2019-05-28 [1] RSPM (R 4.0.0)                           
##  factoextra           * 1.0.7      2020-04-01 [1] RSPM (R 4.0.0)                           
##  fansi                  0.4.1      2020-01-08 [1] RSPM (R 4.0.0)                           
##  farver                 2.0.3      2020-01-16 [1] RSPM (R 4.0.0)                           
##  fastcluster          * 1.1.25     2018-06-07 [1] RSPM (R 4.0.0)                           
##  fastmap                1.0.1      2019-10-08 [1] RSPM (R 4.0.0)                           
##  fastmatch              1.1-0      2017-01-28 [1] RSPM (R 4.0.0)                           
##  fgsea                  1.14.0     2020-04-27 [1] Bioconductor                             
##  filelock               1.0.2      2018-10-05 [1] RSPM (R 4.0.0)                           
##  flextable            * 0.5.10     2020-05-15 [1] RSPM (R 4.0.0)                           
##  forcats              * 0.5.0      2020-03-01 [1] RSPM (R 4.0.0)                           
##  foreach                1.5.0      2020-03-30 [1] RSPM (R 4.0.0)                           
##  foreign                0.8-80     2020-05-24 [2] RSPM (R 4.0.0)                           
##  formattable          * 0.2.0.1    2016-08-05 [1] RSPM (R 4.0.0)                           
##  Formula                1.2-3      2018-05-03 [1] RSPM (R 4.0.0)                           
##  fs                     1.4.1      2020-04-04 [1] RSPM (R 4.0.0)                           
##  furrr                * 0.1.0      2018-05-16 [1] RSPM (R 4.0.0)                           
##  future               * 1.17.0     2020-04-18 [1] RSPM (R 4.0.0)                           
##  gdtools                0.2.2      2020-04-03 [1] RSPM (R 4.0.0)                           
##  genefilter           * 1.70.0     2020-04-27 [1] Bioconductor                             
##  geneplotter            1.66.0     2020-04-27 [1] Bioconductor                             
##  generics               0.0.2      2018-11-29 [1] RSPM (R 4.0.0)                           
##  GenomeInfoDb         * 1.24.2     2020-06-15 [1] Bioconductor                             
##  GenomeInfoDbData       1.2.3      2020-09-18 [1] Bioconductor                             
##  GenomicRanges        * 1.40.0     2020-04-27 [1] Bioconductor                             
##  ggforce              * 0.3.1      2019-08-20 [1] RSPM (R 4.0.0)                           
##  ggplot2              * 3.3.1      2020-05-28 [1] RSPM (R 4.0.0)                           
##  ggplotify            * 0.0.5      2020-03-12 [1] RSPM (R 4.0.0)                           
##  ggpubr               * 0.3.0      2020-05-04 [1] RSPM (R 4.0.0)                           
##  ggradar              * 0.2        2020-09-18 [1] Github (ricardo-bion/ggradar@63e5cef)    
##  ggraph                 2.0.3      2020-05-20 [1] RSPM (R 4.0.0)                           
##  ggrepel              * 0.8.2      2020-03-08 [1] RSPM (R 4.0.0)                           
##  ggridges               0.5.2      2020-01-12 [1] RSPM (R 4.0.0)                           
##  ggsignif               0.6.0      2019-08-08 [1] RSPM (R 4.0.0)                           
##  ggtext               * 0.1.0      2020-06-04 [1] RSPM (R 4.0.0)                           
##  globals                0.12.5     2019-12-07 [1] RSPM (R 4.0.0)                           
##  glue                   1.4.1      2020-05-13 [1] RSPM (R 4.0.0)                           
##  GO.db                  3.11.4     2020-09-18 [1] Bioconductor                             
##  GOSemSim               2.14.2     2020-09-04 [1] Bioconductor                             
##  gower                  0.2.1      2019-05-14 [1] RSPM (R 4.0.0)                           
##  GPfit                  1.0-8      2019-02-08 [1] RSPM (R 4.0.0)                           
##  graphlayouts           0.7.0      2020-04-25 [1] RSPM (R 4.0.0)                           
##  gridBase               0.4-7      2014-02-24 [1] RSPM (R 4.0.0)                           
##  gridExtra              2.3        2017-09-09 [1] RSPM (R 4.0.0)                           
##  gridGraphics           0.5-0      2020-02-25 [1] RSPM (R 4.0.0)                           
##  gridtext               0.1.1      2020-02-24 [1] RSPM (R 4.0.0)                           
##  gtable                 0.3.0      2019-03-25 [1] RSPM (R 4.0.0)                           
##  gtools               * 3.8.2      2020-03-31 [1] RSPM (R 4.0.0)                           
##  haven                  2.3.1      2020-06-01 [1] RSPM (R 4.0.0)                           
##  HGNChelper           * 0.8.1      2019-10-24 [1] RSPM (R 4.0.0)                           
##  Hmisc                  4.4-0      2020-03-23 [1] RSPM (R 4.0.0)                           
##  hms                    0.5.3      2020-01-08 [1] RSPM (R 4.0.0)                           
##  htmlTable              1.13.3     2019-12-04 [1] RSPM (R 4.0.0)                           
##  htmltools              0.4.0      2019-10-04 [1] RSPM (R 4.0.0)                           
##  htmlwidgets            1.5.1      2019-10-08 [1] RSPM (R 4.0.0)                           
##  httpuv                 1.5.4      2020-06-06 [1] RSPM (R 4.0.0)                           
##  httr                   1.4.1      2019-08-05 [1] RSPM (R 4.0.0)                           
##  igraph                 1.2.5      2020-03-19 [1] RSPM (R 4.0.0)                           
##  import                 1.1.0      2015-06-22 [1] RSPM (R 4.0.0)                           
##  impute                 1.62.0     2020-04-27 [1] Bioconductor                             
##  infer                * 0.5.1      2019-11-19 [1] RSPM (R 4.0.0)                           
##  inline                 0.3.15     2018-05-18 [1] RSPM (R 4.0.0)                           
##  ipred                  0.9-9      2019-04-28 [1] RSPM (R 4.0.0)                           
##  IRanges              * 2.22.2     2020-05-21 [1] Bioconductor                             
##  iterators              1.0.12     2019-07-26 [1] RSPM (R 4.0.0)                           
##  janeaustenr            0.1.5      2017-06-10 [1] RSPM (R 4.0.0)                           
##  janitor              * 2.0.1      2020-04-12 [1] RSPM (R 4.0.0)                           
##  jpeg                   0.1-8.1    2019-10-24 [1] RSPM (R 4.0.0)                           
##  jsonlite               1.6.1      2020-02-02 [1] RSPM (R 4.0.0)                           
##  kableExtra           * 1.1.0      2019-03-16 [1] RSPM (R 4.0.0)                           
##  knitr                * 1.28       2020-02-06 [1] RSPM (R 4.0.0)                           
##  labeling               0.3        2014-08-23 [1] RSPM (R 4.0.0)                           
##  later                  1.1.0.1    2020-06-05 [1] RSPM (R 4.0.0)                           
##  lattice              * 0.20-41    2020-04-02 [2] CRAN (R 4.0.0)                           
##  latticeExtra           0.6-29     2019-12-19 [1] RSPM (R 4.0.0)                           
##  lava                   1.6.7      2020-03-05 [1] RSPM (R 4.0.0)                           
##  lazyeval               0.2.2      2019-03-15 [1] RSPM (R 4.0.0)                           
##  lhs                    1.0.2      2020-04-13 [1] RSPM (R 4.0.0)                           
##  lifecycle              0.2.0      2020-03-06 [1] RSPM (R 4.0.0)                           
##  limma                  3.44.3     2020-06-12 [1] Bioconductor                             
##  listenv                0.8.0      2019-12-05 [1] RSPM (R 4.0.0)                           
##  lme4                   1.1-23     2020-04-07 [1] RSPM (R 4.0.0)                           
##  locfit                 1.5-9.4    2020-03-25 [1] RSPM (R 4.0.0)                           
##  loo                    2.2.0      2019-12-19 [1] RSPM (R 4.0.0)                           
##  lubridate              1.7.8      2020-04-06 [1] RSPM (R 4.0.0)                           
##  magrittr               1.5        2014-11-22 [1] RSPM (R 4.0.0)                           
##  markdown               1.1        2019-08-07 [1] RSPM (R 4.0.0)                           
##  MASS                   7.3-51.6   2020-04-26 [2] RSPM (R 4.0.0)                           
##  Matrix               * 1.2-18     2019-11-27 [2] CRAN (R 4.0.0)                           
##  matrixStats          * 0.56.0     2020-03-13 [1] RSPM (R 4.0.0)                           
##  memoise                1.1.0      2017-04-21 [1] RSPM (R 4.0.0)                           
##  mgcv                 * 1.8-31     2019-11-09 [2] CRAN (R 4.0.0)                           
##  mime                   0.9        2020-02-04 [1] RSPM (R 4.0.0)                           
##  miniUI                 0.1.1.1    2018-05-18 [1] RSPM (R 4.0.0)                           
##  minqa                  1.2.4      2014-10-09 [1] RSPM (R 4.0.0)                           
##  ModelMetrics           1.2.2.2    2020-03-17 [1] RSPM (R 4.0.0)                           
##  modelr                 0.1.8      2020-05-19 [1] RSPM (R 4.0.0)                           
##  moduleScoreR         * 0.0.0.9200 2020-09-18 [1] Github (milescsmith/moduleScoreR@e6db70f)
##  munsell                0.5.0      2018-06-12 [1] RSPM (R 4.0.0)                           
##  nlme                 * 3.1-148    2020-05-24 [2] RSPM (R 4.0.0)                           
##  nloptr                 1.2.2.1    2020-03-11 [1] RSPM (R 4.0.0)                           
##  NMF                    0.22.0     2020-02-12 [1] RSPM (R 4.0.0)                           
##  nnet                   7.3-14     2020-04-26 [2] RSPM (R 4.0.0)                           
##  officer                0.3.11     2020-05-18 [1] RSPM (R 4.0.0)                           
##  openxlsx               4.1.5      2020-05-06 [1] RSPM (R 4.0.0)                           
##  paletteer            * 1.2.0      2020-06-07 [1] RSPM (R 4.0.0)                           
##  parsnip              * 0.1.1      2020-05-06 [1] RSPM (R 4.0.0)                           
##  pheatmap             * 1.0.12     2019-01-04 [1] RSPM (R 4.0.0)                           
##  pillar                 1.4.4      2020-05-05 [1] RSPM (R 4.0.0)                           
##  pkgbuild               1.0.8      2020-05-07 [1] RSPM (R 4.0.0)                           
##  pkgconfig              2.0.3      2019-09-22 [1] RSPM (R 4.0.0)                           
##  pkgmaker               0.31.1     2020-03-19 [1] RSPM (R 4.0.0)                           
##  plotly               * 4.9.2.1    2020-04-04 [1] RSPM (R 4.0.0)                           
##  plyr                   1.8.6      2020-03-03 [1] RSPM (R 4.0.0)                           
##  png                    0.1-7      2013-12-03 [1] RSPM (R 4.0.0)                           
##  polyclip               1.10-0     2019-03-14 [1] RSPM (R 4.0.0)                           
##  preprocessCore         1.50.0     2020-04-27 [1] Bioconductor                             
##  prettyunits            1.1.1      2020-01-24 [1] RSPM (R 4.0.0)                           
##  prismatic              0.2.0      2019-12-01 [1] RSPM (R 4.0.0)                           
##  pROC                   1.16.2     2020-03-19 [1] RSPM (R 4.0.0)                           
##  processx               3.4.2      2020-02-09 [1] RSPM (R 4.0.0)                           
##  prodlim                2019.11.13 2019-11-17 [1] RSPM (R 4.0.0)                           
##  progress               1.2.2      2019-05-16 [1] RSPM (R 4.0.0)                           
##  promises               1.1.0      2019-10-04 [1] RSPM (R 4.0.0)                           
##  ps                     1.3.3      2020-05-08 [1] RSPM (R 4.0.0)                           
##  purrr                * 0.3.4      2020-04-17 [1] RSPM (R 4.0.0)                           
##  qvalue                 2.20.0     2020-04-27 [1] Bioconductor                             
##  R6                     2.4.1      2019-11-12 [1] RSPM (R 4.0.0)                           
##  randomForest         * 4.6-14     2018-03-25 [1] RSPM (R 4.0.0)                           
##  RColorBrewer         * 1.1-2      2014-12-07 [1] RSPM (R 4.0.0)                           
##  Rcpp                   1.0.4.6    2020-04-09 [1] RSPM (R 4.0.0)                           
##  RCurl                  1.98-1.2   2020-04-18 [1] RSPM (R 4.0.0)                           
##  readr                * 1.3.1      2018-12-21 [1] RSPM (R 4.0.0)                           
##  readxl               * 1.3.1      2019-03-13 [1] RSPM (R 4.0.0)                           
##  recipes              * 0.1.12     2020-05-01 [1] RSPM (R 4.0.0)                           
##  registry               0.5-1      2019-03-05 [1] RSPM (R 4.0.0)                           
##  rematch2               2.1.2      2020-05-01 [1] RSPM (R 4.0.0)                           
##  reprex                 0.3.0      2019-05-16 [1] RSPM (R 4.0.0)                           
##  reshape2               1.4.4      2020-04-09 [1] RSPM (R 4.0.0)                           
##  rio                    0.5.16     2018-11-26 [1] RSPM (R 4.0.0)                           
##  rlang                * 0.4.6      2020-05-02 [1] RSPM (R 4.0.0)                           
##  rmarkdown              2.2        2020-05-31 [1] RSPM (R 4.0.0)                           
##  rngtools               1.5        2020-01-23 [1] RSPM (R 4.0.0)                           
##  rpart                  4.1-15     2019-04-12 [2] CRAN (R 4.0.0)                           
##  rsample              * 0.0.7      2020-06-04 [1] RSPM (R 4.0.0)                           
##  rsconnect              0.8.16     2019-12-13 [1] RSPM (R 4.0.0)                           
##  RSQLite                2.2.0      2020-01-07 [1] RSPM (R 4.0.0)                           
##  rstan                  2.19.3     2020-02-11 [1] RSPM (R 4.0.0)                           
##  rstanarm               2.19.3     2020-02-11 [1] RSPM (R 4.0.0)                           
##  rstantools             2.1.0      2020-06-01 [1] RSPM (R 4.0.0)                           
##  rstatix              * 0.6.0.999  2020-09-18 [1] Github (milescsmith/rstatix@6f5e0a6)     
##  rstudioapi             0.11       2020-02-07 [1] RSPM (R 4.0.0)                           
##  rsvd                   1.0.3      2020-02-17 [1] RSPM (R 4.0.0)                           
##  rvcheck                0.1.8      2020-03-01 [1] RSPM (R 4.0.0)                           
##  rvest                  0.3.5      2019-11-08 [1] RSPM (R 4.0.0)                           
##  S4Vectors            * 0.26.1     2020-05-16 [1] Bioconductor                             
##  scales               * 1.1.1      2020-05-11 [1] RSPM (R 4.0.0)                           
##  scatterpie             0.1.4      2019-11-08 [1] RSPM (R 4.0.0)                           
##  sessioninfo            1.1.1      2018-11-05 [1] RSPM (R 4.0.0)                           
##  shiny                  1.4.0.2    2020-03-13 [1] RSPM (R 4.0.0)                           
##  shinyjs                1.1        2020-01-13 [1] RSPM (R 4.0.0)                           
##  shinystan              2.5.0      2018-05-01 [1] RSPM (R 4.0.0)                           
##  shinythemes            1.1.2      2018-11-06 [1] RSPM (R 4.0.0)                           
##  snakecase              0.11.0     2019-05-25 [1] RSPM (R 4.0.0)                           
##  snow                   0.4-3      2018-09-14 [1] RSPM (R 4.0.0)                           
##  SnowballC              0.7.0      2020-04-01 [1] RSPM (R 4.0.0)                           
##  StanHeaders            2.21.0-3   2020-05-28 [1] RSPM (R 4.0.0)                           
##  statmod                1.4.34     2020-02-17 [1] RSPM (R 4.0.0)                           
##  storr                  1.2.1      2018-10-18 [1] RSPM (R 4.0.0)                           
##  stringi                1.4.6      2020-02-17 [1] RSPM (R 4.0.0)                           
##  stringr              * 1.4.0      2019-02-10 [1] RSPM (R 4.0.0)                           
##  SummarizedExperiment * 1.18.2     2020-07-09 [1] Bioconductor                             
##  survival               3.1-12     2020-04-10 [2] CRAN (R 4.0.0)                           
##  sva                  * 3.36.0     2020-04-27 [1] Bioconductor                             
##  systemfonts            0.2.2      2020-05-14 [1] RSPM (R 4.0.0)                           
##  threejs                0.3.3      2020-01-21 [1] RSPM (R 4.0.0)                           
##  tibble               * 3.0.1      2020-04-20 [1] RSPM (R 4.0.0)                           
##  tidygraph              1.2.0      2020-05-12 [1] RSPM (R 4.0.0)                           
##  tidymodels           * 0.1.0      2020-02-16 [1] RSPM (R 4.0.0)                           
##  tidyposterior          0.0.2      2018-11-15 [1] RSPM (R 4.0.0)                           
##  tidypredict            0.4.5      2020-02-10 [1] RSPM (R 4.0.0)                           
##  tidyr                * 1.1.0      2020-05-20 [1] RSPM (R 4.0.0)                           
##  tidyselect           * 1.1.0      2020-05-11 [1] RSPM (R 4.0.0)                           
##  tidytext               0.2.4      2020-04-17 [1] RSPM (R 4.0.0)                           
##  tidyverse            * 1.3.0      2019-11-21 [1] RSPM (R 4.0.0)                           
##  timeDate               3043.102   2018-02-21 [1] RSPM (R 4.0.0)                           
##  tokenizers             0.2.1      2018-03-29 [1] RSPM (R 4.0.0)                           
##  triebeard              0.3.0      2016-08-04 [1] RSPM (R 4.0.0)                           
##  tune                 * 0.1.0      2020-04-02 [1] RSPM (R 4.0.0)                           
##  tweenr                 1.0.1      2018-12-14 [1] RSPM (R 4.0.0)                           
##  tximport             * 1.16.1     2020-06-05 [1] Bioconductor                             
##  txtq                   0.2.0      2019-10-15 [1] RSPM (R 4.0.0)                           
##  urltools               1.7.3      2019-04-14 [1] RSPM (R 4.0.0)                           
##  uuid                   0.1-4      2020-02-26 [1] RSPM (R 4.0.0)                           
##  uwot                 * 0.1.8      2020-03-16 [1] RSPM (R 4.0.0)                           
##  vctrs                  0.3.1      2020-06-05 [1] RSPM (R 4.0.0)                           
##  viridis              * 0.5.1      2018-03-29 [1] RSPM (R 4.0.0)                           
##  viridisLite          * 0.3.0      2018-02-01 [1] RSPM (R 4.0.0)                           
##  webshot                0.5.2      2019-11-22 [1] RSPM (R 4.0.0)                           
##  WGCNA                * 1.69       2020-02-28 [1] RSPM (R 4.0.0)                           
##  withr                  2.2.0      2020-04-20 [1] RSPM (R 4.0.0)                           
##  workflows            * 0.1.1      2020-03-17 [1] RSPM (R 4.0.0)                           
##  xfun                   0.14       2020-05-20 [1] RSPM (R 4.0.0)                           
##  XML                    3.99-0.3   2020-01-20 [1] RSPM (R 4.0.0)                           
##  xml2                   1.3.2      2020-04-23 [1] RSPM (R 4.0.0)                           
##  xtable                 1.8-4      2019-04-21 [1] RSPM (R 4.0.0)                           
##  xts                    0.12-0     2020-01-19 [1] RSPM (R 4.0.0)                           
##  XVector                0.28.0     2020-04-27 [1] Bioconductor                             
##  yaml                   2.2.1      2020-02-01 [1] RSPM (R 4.0.0)                           
##  yardstick            * 0.0.6      2020-03-17 [1] RSPM (R 4.0.0)                           
##  zip                    2.0.4      2019-09-01 [1] RSPM (R 4.0.0)                           
##  zlibbioc               1.34.0     2020-04-27 [1] Bioconductor                             
##  zoo                    1.8-8      2020-05-02 [1] RSPM (R 4.0.0)                           
## 
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library